Comparison of gut microbiota in exclusively breast-fed and formula-fed babies: a study of 91 term infants

Abstract

To compare gut microbiota of healthy infants that were exclusively breast-fed or formula-fed, we recruited 91 infants, who were assigned into three different groups and fed by breast milk (30 babies), formula A (30 babies) or formula B (31 babies) exclusively for more than 4 months after birth. Faecal bacterial composition was tested. Among different groups, α diversity was lower in breast-fed group than formula-fed groups in 40 days of age, but increased significantly in 6 months of age. The Bifidobacterium represented the most predominant genus and Enterobacteriaceae the second in all groups. In 40 days of age, Bifidobacterium and Bacteroides were significantly higher, while Streptococcus and Enterococcus were significantly lower in breast-fed group than they were in formula A-fed group. Lachnospiraceae was lower in breast-fed than formula B-fed group. Veillonella and Clostridioides were lower in breast-fed than formula-fed groups. In 3 months of age there were less Lachnospiraceae and Clostridioides in breast-fed group than formula-fed groups. There were also significant differences of microbiota between formula A-fed and formula B-fed groups. Those differences may have impacts on their long-term health.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1

α diversity measurements using Ace index values indicated gut microbiota abundance (A), and Shannon index values indicated gut microbiota diversity (B). Y-axis represents the values of ACE (A) or Shannon index (B). Boxplots compare α diversity of gut microbiota in 40 days (40 d), 3 months (3 m), and 6 months (6 m) of age among breast-fed group, formula A-fed group, and formula B-fed group. Boxes show 25th to 75th percentiles and the median line, and whiskers indicate minimum to maximum values. Statistical significance was evaluated by Wilcoxon test, using p ≤ 0.05 as the measure of significance.

Figure 2

β diversity measurements by Unweighted UniFrac (A) and Weighted UniFrac (B). Boxplots compare β diversity of gut microbiota in 40 days (40 d), 3 months (3 m), and 6 months (6 m) of age among breast-fed group, formula A-fed group, and formula B-fed group. Boxes show 25th–75th percentiles and the median line, and whiskers indicate minimum to maximum values. Statistical significance was evaluated by Wilcoxon test, using p ≤ 0.05 as the measure of significance.

Figure 3

The OTUs heatmap at genus level. The relative abundance of OTUs was assessed across all samples, and OTUs were clustered in a heatmap according to their co-occurrence at genus level. Clustering was performed as a type of hierarchical clustering method to interpret the distance matrix using average linkage. The dendrogram provides the genus designation along the right Y-axis and the abundance relationship across all samples for each genus along the left Y-axis. The colour scale for the heatmap is shown in the upper right corner of the figure.

Figure 4

The ten most abundant bacteria of gut microbiota at genus level. Relative abundance estimates of the ten most dominant bacteria at genus level in 40 days, 3 months, and 6 months of age among breast-fed group, formula A-fed group, and formula B-fed group.

Figure 5

Gut microbiota comparison among different groups in 40 days of age. Bar graphs showing the relative abundance of the bacteria at genus level from breast-fed group, formula A-fed group, and formula B-fed group in 40 days of age. Variables were statistically tested by a two-tailed t test.

Figure 6

Gut microbiota comparison among different groups in 3 months of age. Bar graphs showing the relative abundance of the bacteria at genus level from breast-fed group, formula A-fed group, and formula B-fed group in 3 months of age. Variables were statistically tested by a two-tailed t test.